Military Secrets
by ArizonaRoseWolf
Summary: Fill involving John being a specially trained soldier.
1. Chapter 1

**Another fill, I just couldn't resist this. Especially not after one of the comments said "John is the British!MacgGyver" I died inside at that. **

**This is the prompt:**

**John was part of an elite military team in Afghanistan, trained to be silent, deadly, and uncatchable.  
Now Sherlock is investigating a series of murders that bear the signature of a man John worked alongside in the war. As possibly the only person capable of catching the killer, John must do so whilst also keeping Sherlock safe, arguing with Mycroft, and keeping Scotland Yard from screwing the whole thing up.**

**John/Sherlock, or Lestrade, or Mycroft, or any other combination thereof, I'm not picky.**

**TL;DR: bamf!John has to track down a former army teammate who's killing folk.**

John crouched over the body, frowning deeply. He recognized the style of killing and was silently berating himself for not realizing it earlier. He absentmindedly rubbed his shoulder. Then the deep voice of his flatmate and friend interrupted his thoughts, making him jump. "Your opinion on the body John. We don't have all day."

John didn't take Sherlock's irritability personally, he was just annoyed because Scotland Yard had waited until the sixth body to finally call Sherlock in. John sighed, stood, turned to Sherlock, and said, "You shouldn't continue this case."

Silence filled the dusty room of the warehouse they were in. Seeing as John had never told Sherlock to drop a case, it was understandable. Sherlock's icy, "What?" was followed by his intense gaze scanning John's body. Sherlock looked shocked when he couldn't read John. He scanned him again with the same result.

John turned to Lestrade and said calmly but firmly, "Get everyone off the scene and have someone bring the files of the last five to me. I expect no one to here inside the tape when I get back. I have to make a phone call."

And with that, John was off. They just caught the beginning of John sending orders into the phone. "Genny, I need you, Rover, and Flight to-"

Lestrade blinked and then said, "Did John Watson just tell me to get off my crime scene?"

"Yes detective inspector, and you will be going to the other side of the tape." Mycroft said as he stepped from the shadows.


	2. Chapter 2

**I'm baaaack! Ok, so, I have absolutely no idea where I'm going with this and I have no beta (not to mention I'm not sure how betas work) so if someone could explain how betas work, I would love them forever. Also, if you have any prompts for John's time in Afghanistan I would love to take a stab at them, however, I ask that you send them through review because I keep forgetting about private messaging. Aaanywaaays, on to the story. ;)**

Sherlock whirled to face Mycroft and demanded, "What is this? Why is John hijacking _my_ crime scene?"

Mycroft smiled icily. "Brother dear, I'm afraid that is for Captain Watson to tell you."

"What does John's rank have to do with this?" Lestrade demanded angrily. "And why the _hell_ does that mean I have to get off my crime scene."

Mycroft smirked and said, "Oh my, why must the two of you always be so... possessive?"

"Alright, Mycroft, that's enough." John had come back from his phone call. He then turned to Lestrade and said, "Why isn't this scene clear of all Yarders? This is above your pay grade. And your security access. Now-"

"And its not above yours?" Sherlock snorted. "I find that hard to believe. You were a soldier, your security access can't possibly be above mine."

"It is. Quite a ways above yours, actually. Priority Ultra." Sherlock blinked. Then why hadn't he used it at Baskerville? As if he'd read Sherlock's mind (a Truly Scary concept), John added, "And I didn't use it at Baskerville because I was still hoping we would get kicked out before anyone there recognized me."

"Why would anyone at a top secret (although not actually that secret, just highly classified) government lab?" Sherlock drawled lazily.

John hesitated before straightening and falling easily into parade rest. "Because that's where I became who I am."

"And who are you?" Donovan, who had been silently listening the whole time, sneered.

John looked directly at Donovan, who shrank back from his inhuman gaze, and replied with a quiet firmness that had Sherlock tensing, said, "The single most dangerous man you have ever met."

"And that is?" Sherlock inquired was Mycroft who replied.

"An Elite Forces Hunter."

**Thank you for the reviews, and explaining betas to me, I will try and write more soon. However, my brain is currently offline. It decided that it didn't want to do anything after an intro to a foreign language. Anyways, I'm going to try and write more either later today or tomorrow. Oh, and I fixed the mistake, it's no longer "she gang back" it's now "she shrank back."**


	3. Chapter 3

**I've decided that if I do a sequel/prequel to this, I'll be letting you know by the 8th chapter. In the meantime, I do hope you enjoy reading this.**

Sherlock blinked. "And what is an Elite Forces Hunter?"

John sighed and said, " No, Mycroft, not Elite Forces Hunter. I am part of the Elite Forces, and my job title is Hunter. They're not all said together. You say either Elite Forces or Hunter. Not both."

Mycroft huffed and, with a sour expression on his face, apologised (which was surely a sign of the apocalypse because Mycroft-I'm-oh-so-important-bow-before-my-intellec tual-prowess-Holmes did not _apologise_). "My apologies, John."

"And you should be addressing me as Captain, seeing as I'm now working."

"...vey well, _Captain_."

"Who are you and what have you done with my annoying prat of a brother?!" Sherlock demanded. Mycroft was never one to address "lesser" people.

"He's still Mycroft, no need to worry. He just has to behave himself because he owes me and therefore works for me until the debt is paid." John cut in.

"Owes you how?" Lestrade inserted. "And what gives you the right to kick us of the crime scene?"

John sighed, and when he spoke again, the hairs on the backs of everyone's necks stood up. He sounded less human in a way that made him dangerous. He didn't raise his voice. It was like the calm three seconds before you go para shooting. The moment when you think "Oh. This is actually happening, I'm about to fall eighteen hundred feet out of a plane." But all he said was, "I know who, how, and most importantly, why. Get off this scene because you do not want to face the person who created it."

"And what makes you say that?" Anderson demanded snidely.

"He's one of us." They all turned to find three people in camoflage cargo pants and black t-shirts with various weapons and gear on them. The woman who had spoken stepped forward and said, "He's your worst nightmare, you just don't know it yet."


	4. Chapter 4

**Ok, so I think I've kinda got an idea of where I'm going but I still don't know so this should be interesting...aaaaaanywaaaaaysss: please review, they makes me happy and so I write faster.**

The woman stepped carefully around the body, slapped John, pointed at him, and said, "That's for not contacting me until now."

"You know why I didn't. Cold turkey." John replied calmly.

"When Joker suggested that to you, he didn't mean Cold Turkey us. He meant lay off the life-threatening missions." Flight interrupted smoothly. But that's not the point. The point is Blake's lost a few more screws since we last saw him."

"And we need type to find him." Rover finished.

"I haven't Hunted in three years."

"Yes you have." Genny cut in. "You Hunted the cabbie. From the first case you worked with your-"

"Say boyfriend and I will slap you upside the head."

Genny put on an innocent face and said, "So he's not?"

"No."

"Then can I have him?"

"No."

"Awww, but-"

"No. Just no. You are _not_ doing this _again_. We are not having a repeat of Geneva. I _refuse_. N-O. _No_. Not ha-"

"I think she gets it." Flight cut in. "Now will you Hunt?"

"I don't-"

"You can do it, TC." Rover said softly. "Please. For Queen and Country."

John sighed. That was the one argument John had a hard time saying no to. It was practically his motto, after In Arduis Fidelis. But it'd been years since he Hunted and his last Hunt had been bad. He'd been shot, tortured, and left out in the desert to die of dehydration and sunstroke. "What do you think, Genny." He asked quietly, already knowing the answer.

"You know what I think." She said gently. Genny pulled him into a hug and said, "I think we need you, more importantly we want you. But most important of all: you are our family, we want you to be happy."

John leant into Genny (she was about a head taller than him, thin , muscular, and black hair pulled into a bun). He murmured into her shoulder, "I'll hunt."

"Wait, hold up. You shot the cabbie? _You_? Way-too-"honourable"-for-his-own-good-Watson?" Donovan cut in angrily. "Who _are_ you? What makes you think you can get away with murder? We're gunna have to take you in."

Flight, Rover, Genny, Sherlock, and even Mycroft were suddenly between John and Sally. It was Genny who said, "You ain't takin him nowhere! He stayin with us. He has one-a them "license to kill" thangs."

"Tone it down Genny, you're accent 's coming out strong." John said calmly. "And no, you won't be taking me anywhere. Permission to Hunt General?"

"Permission granted." Genny said formally.

John bent to the crime scene, examining it from as many angles as possible before taking off. Genny, Rover, and Flight following quickly.

Anthea walked over to Mycroft and said, "What did I miss?"

Mycroft just chuckled under his breath and said, "Come. John is on the Hunt."


	5. Chapter 5

**So I just realised that I haven't done a disclaimer for this yet. I don't own Sherlock, sadly, I never will. Although that's probably a flood thing. Thank you for reviewing. ;) **

**Also, this is gunna have a little bit of John's thought process from the very end of the last chapter.**

John dropped down beside the body and felt his mind shift. He felt traces of the aura of his once friend and blinked slowly. Then he was off, racing through the warehouse, out the back door, up a nearby fire escape, across a roof, through an open window, past trees and bricks and sewer. He ran as fast as he could, pushing himself hard, a corner of his mind revealing in the feeling of his feet pounding against the ground.

The aura was getting stronger and John went faster, still. He could sense the menace in it and the intent to take another life soon. He dove into the traffic, running alongside cars before jumping lightly onto the roof of a moving taxi. He stood, feeling the wind whipping through his hair, and thought of a time long ago, when he was still learning. When he was transferring from hunted to Hunter.

When the aura was so strong he could almost taste it, he stopped and shouted, "_Come out here! Face me like a man, you back-stabbing son of a bastard! You know it's me you_ _want_!"

"Help!" John feel his face blanch. The monster had a kid. John surged forward, breaking down the door of an ordinary-looking apartment building. He stood there with an arm around the little girl's throat, a sadistic grin around his face.

"Let her go." John do his best not to jump. He hasn't realised that Genny, Rover, Flight, and Sherlock (How had Sherlock managed to keep up?) had followed him.

"I don't see why I should. She's the perfect weapon to use against you." His voice was just as grating as ever.

"Let her go, Nightbrook."

"No! I told you NO! I am not Nightbrook! I'm not I'm not I can't be! Nightbrook is _dead_! He died when Sheila did! Sheila was his other half! He loved her. He bonded her! He died when she did and don't you _dare_ say otherwise!" The man screeched, letting go of the girl and clutching at his ears.

Flight darted forward and grabbed her, tugging her to his chest. Rover grabbed Sherlock, Genny grabbed John, and John shouted, "RUN!"

They burst out of the door to the apartment and dove to the ground, just as the building went imploded, crumpling in on itself before exploding outward. Rover tossed up an arm and Shielded them. Once the groaned stopped groaning, Rover let go of Sherlock and sat up. Sherlock looked over to John accusingly and said, "And _you_ said chasing a cab across London was the craziest thing you ever did. Now I don't know if you've _noticed_ but that was _a whole other level of crazy right there."_

Flight uncurled from around the girl and turned to look at Genny, who got off of John and then started giggling. John, Rover, Flight and Sherlock joined in until they were leaning against each other like puppies and crying from the force of their laughter.


	6. Chapter 6

**Hi guys! Sorry this chapter took me so long, life got in the way. Anywaaaays, I've not made my decision about a prequel yet and I want to hear your opinion on it seeing as I told you I'd decide by the 8th chapter...so please, opinions people! And thank you those of you who have reviewed. ;)**

As the giggles died down, John turned to the girl and said, "What's your name?"

She remained silent and shook her head. Flight, who still had a close hold on her, asked, "Do you know a way to get into contact with any family you might have?" Again she shook her head.

Sherlock looked between John and the girl, wanting to blurt out his deductions but something held him back. He hadn't known John could run that fast, it shouldn't have been possible for an ex-army doctor who used to have a psychosomatic limp. John seemed to become more dangerous with each minute he spent with these people. And it bothered him that he couldn't deduce any of them. That just didn't happen. There was always something. But with them it was Nothing. He couldn't even tell what they'd had for breakfast this morning (except John but that's only because John made him eat breakfast, too.).

"Sherlock!" John said in that tone that indicated that he'd called Sherlock's name repeatedly. Sherlock gave him a questioning look and John reiterated, "What've you got, Sherlock?"

"On?"

"Brit."

"Who?"

"The _girl_, Sherlock. The one currently sitting in Flight's lap."

Sherlock glanced over at her again and frowned before saying sarcastically, "_Brit_ is the _best_ you can do? Honestly, John, surely that wasn't from you. It's much to plain, although her real name isn't much better. What parent names their child _Lake_? It's utterly depressing, the IQ of ordinary people. She's the middle child of three kids, has been living homeless for three weeks, hasn't eaten in two days, is in desperate need of a bath, used to be locked in a closet on a daily basis, and is terrified that you're going to turn her into the authorities because they will try and make her go to another foster home. But that's not what she needs or wants. I suggest the orphanage near the town where I grew up. It's a good place and the woman who owns it owes me a favor."

Sherlock took a deep breath, trying to calm himself. He felt off, as though the world wasn't quite the way it normally is. John was hiding things from him, strangers were taking over his case, the little girl someone had named Brit had crawled out of "Flight's" lap and onto his, and the world was spotty. Or was that his vision? Something wasn't quite right.

He felt himself listing to the side. He was vaguely aware of someone saying something to him but he couldn't respond. The world faded to the black vat of unconsciousness.

...

Lake crawled over to the man who had put into words what she couldn't say. Nobody wanted a strange child. She lay down, leaning her upper body on to his lap and burying her face in his stomach. But there was something wrong with the man. The guy who had asked her name was moving her out of the way and saying, "Sherlock? Sherlock? Answer me! _Sherlock_!"

Then he slapped the blunt man. Lake flew at him, scratching at his eyes as her mamma had showed her. She bit his wrist when he tried to pull her off. Other hands grabbed her but she screamed and fought till they let her go. She ran to the man and crouched over him. He wasn't moving.

Lake grabbed his temples and dove into his mind. She found the wrong place and set to fixing it. The scary man who had grabbed her of the street had done something to his mind. He was in a Night Terror. And she had to save him. She couldn't save her mamma but she would save this man. She had to.


	7. Chapter 7

**Warning: mentions, and descriptions, of child neglect/abuse. I'm sorry if you hate reading it but it's something that will be crucial to the story later.**

John watched closely as the girl Sherlock had named as Lake leaned over him and put her hands to his temples. It was remarkably familiar. He scanned his brain to try and think of who would have done that.

Sherlock arched slightly, as if trying to get away from her but the girl slung a leg over his chest and hung on. The sound of sirens reached him and Genny grabbed his elbow, whispering in his ear, "We need to get out of here. Flight commandeered a taxi. We need to move them.

John nodded, "I'll get his shoulders, you grab his feet."

Lake was aware that they were moving but focused mostly on the man she was Healing. She knew the people moving them were like her mamma. She didn't know how she knew but she did. She ducked her head when they manouvred into the taxi. Moving them couldn't have been easy.

The man's mind was a dark one. She felt sad that his father had been like her stepfather. Cruel.

Sherlock screamed. He screamed as loud as he could but he couldn't hear anyone. Of course he didn't. His father was always careful to punish him when no one else would hear. He said his mum didn't have the heart for it and his brother didn't care.

Sherlock sank down to the bottom of the door and banged his head against it, repeatedly. He waited and waited but no one came. He was vaguely aware that more time than was usual had passed, but only because he had started to feel hungry.

Personally, he thought the whole thing would be more bearable if he even knew what he'd done wrong. But no one ever told him. Not that he'd asked anyone. He wasn't stupid, asking what he did would just get him more time in the closet.

His skin was crawling with the need to escape. He hated small spaces and this was most definitely a small place. Six paces across, six paces long. It felt like he was slowly being crushed, ion by ion, so that one day he would just disappear.

Time passed, he wasn't sure how long, but suddenly he heard voices. Angry voices, arguing. It sounded like they were arguing about him but he wasn't sure. His head felt like how someone's feels after they eat to much on Thanksgiving. Heavy and slow.

He was vaguely aware of the door bursting open and strangers grabbing him, but he was too weak to fight. They stuck a needle in his arm and he kicked out, hitting one person, but he couldn't tell where the blow landed. He was so tired. Just before the world faded, he caught a glimpse of a little girl with a dirty face and a sad smile. He heard her say, "Hold on, I'll get you out of this."


	8. Chapter 8

**I'm sorry I'm updating so slow. Real Life slapped me in the face again and I have the ACT and the ASVAB within two weeks of each other so my writing may get a little whacky. I apologise in advance. I think I'm going to try and assign days to update stories which means that this story is Thursdays, AtL will be Fridays, and TC will be Tuesdays or whenever the inspiration hits (I'm still tryina catch up with the prompts in that one and failing miserably, I am sorry and will do your prompts, I promise.) Dear me, this is a ridiculous Author's Note, my apologies.**

Lestrade and John carried Sherlock and the girl out of the Cab and into 221B. Mrs Hudson fluttered around them and insisted that they put them in the spare bedroom in her flat rather than try and carry them up the stairs.

Once placed on the bed, John and Lestrade watched as Sherlock started tossing his head and trying to throw the girl. _Hold him down_. Lestrade jumped badly at the voice that sounded in his mind but John seemed unaffected. He grabbed Sherlock's shoulders and nodded at Lestrade to grab his feet. Lestrade moved as Sherlock tried to buck both John and the girl off and nearly succeeded. For a moment, Lestrade was struck by how similar this was to Sherlock's drug days. If you discluded the girl and John.

Sherlock let out a whimper and then started chanting "no" and rolling his head again. The girl finally let go of his head, drew back a little, and then slapped him so hard Mrs. Hudson heard it from the next room even though the door was closed. Sherlock sat up like one of those blow up punching bags in cartoons that get punched then pop back up.

The girl fell into his lap and John lost his grip on his arms. "What_ the hell_ was that for?" Lestrade demanded.

Sherlock stared at the girl wordlessly for a moment before gathering her in a hug and clinging to her like she was a teddy bear. The girl pushed him till he was laying flat, lay her head on his chest, and said softly, "Sleep."

He did.


	9. Chapter 9

**So sorry I'm a day late. I'll make up for it with a long chapter that involves John bossing Mycroft around and a short author's note. Thanks for reading!**

...

John sat down on the couch so he could watch the girl and Sherlock. Let's trade sat down in John's chair and stared at John. "You want an explanation."

Out of the corner of his eye, John saw Lestrade dip his head in wary acknowledgement. John huffed a tired laugh said rubbed his temples. "It's a long story, over half of it's classified, and the part that isn't doesn't make much since without the classified part."

"My security clearance is Beta 7."

"Mine is Priority Ultra." Lestrade turned his head sharply, staring at John suspiciously. "You're just a soldier, how could you possibly get clearance that high?"

"Because I am anything _but _'just a soldier.' There is so much that goes on behind closed doors that over half of all the politicians don't know." John lets out a humorless chuckle.

"And what would give you clearance?"

"That in and of itself is classified."

"Earlier you told Mycroft what to do. And he listened."

"..."

"You can at least tell me why, right?"

"Because he works for me."

"But he kidnaps you and you don't tell him to stop?"

"He works for me unofficially?"

"Are you asking a question or are you answering my question?" Lestrade demanded angrily.

John gave him his Look before saying, "I saved him, he tried to recruit me, I threatened to kill him, he backed off, when someone threatened the Queen he ended up being placed under my command and its been like that since. When it comes to certain issues, I am in charge. In other instances, he is."

"And this instance was national security...how?"

"..."

"Why did you tell Sherlock to drop the case? Wouldn't he be able to help you?"

"I told him to drop it because I knew something like this would happen. I didn't, however, know of that little girl's existence or her ability to help him."

"Why can she help him and not us?"

"Because of N- the man I talked to."

"The slightly insane looking guy?"

"He is not slightly in sane, he is completely insane. If you ever see him on the street, get as far away as possible as soon as possible. He is not to be trifles with and he will be extremely ticked at me."

"Why?"

"Because I'm spoiling his fun."

"How?"

"..."

"Are you just going to refuse to answer when I ask you something you don't want to answer?"

"..."

"So that's a yes?"

"..."

"Okay then."

The door to the stairs opened and in walked Mycroft. "John what happened? Where is Sherlock" What-"

The doctor had straightened and shifted to the Soldier. "It's Captain Watson, Mr Holmes. Your brother will be fine, Lestrade has some questions that I'm sure he would like the answers to. Raise his security status to Alpha 3, I'll be needing him and his two most trustworthy coworkers so have him call them and bring them here. Keep them downstairs while I make a couple of phone calls. Do not interrupt the girl while she is with Sherlock."

Mycroft nodded swiftly and pulled out his phone. "Tell Atlis to come up as well. I'll be needing her specific skillset."

"Of course, Captain." Mycroft said coolly.

And with that John was gone.


	10. Chapter 10

**So I had an interesting review...and I rather liked it. In answer, I'll say this: how do I get a Beta? Is my grammar really bad? Yes I realize I need to go more in depth with John's past, that will be next chapter because I have the ASVAB tomorrow and so actually need sleep. However, if I'm up for it, I'll update this again Saturday. I make no promises on that.**

John walked out the door and down the steps before coming to a stop just outside Mrs. Hudson's doorway. He could already feel it coming. The nasty little side-effect that came from using his '_gift_' without prepping first. The first tremors went down his spine, leaving goosebumps in their wake.

He leaned his head against The door leading to outside and focused on regulating his breathing. "Everything all right, dear?"

John jumped and whirled around. Had he not lost his balance, he would have said he was fine. Had he not hit his spine against the edge of the door frame, he would have just walked outside. But he did, and he couldn't stop his back from arching or his throat from making a squeaking hiss. He couldn't stop the pain from triggering his reflexes and he most definitely could not help the flight reaction that came from memories triggered by the night's events.

John didn't think, he didn't even pause to open the door like a normal person. No, instead he ended up going through it. Ignoring the splinters in his hands and shoulders, he ran. He left Mrs. Hudson startled in the doorway, he left Lestrade and Mycroft's tense silence in the living area, and he left Lake watching over Sherlock as her mother had watched over John himself.


	11. Chapter 11

**MUY IMPORTANTE! The chapter after this has three potential paths:**

**1st one John has a flashback and you learn some things. 2nd one Sherlock wakes up. 3rd one both. You get a say so please review! Thanks To those of you who have reviewed already ^^**

**Also, on a side note, I'm debating on whether or not I should make Mrs. Hudson a main character in this, so if you could give me your opinion on that as well, that would be nice.**

Martha Hudson was no idiot. She knew full well that such a thing as witch craft didn't exist. However, she found herself seriously reconsidering her knowledge and outlook on the world as she watched a tiny slip if a girl supposedly heal Sherlock.

Lestrade and Mycroft had both come running when John had smashed through the door (the poor dear was most definitely going to have splinters), and she had demanded an explanation.

As Martha stood watching Sherlock, she became aware of the little girl staring at her. "Oh, sorry, am I distracting you?"

_Come closer_.

She started badly at the voice in her head but obeyed it anyway. Once she was close enough, the girl took her hand and pulled her to where she was seated at the edge of the bed.

_He needs you._

Martha remained still for a moment. What could she possibly do to help? Sherlock whimpered and tossed his head. Without even pausing to think, she had his head in her lap and was stroking his hair, murmuring soothing nothings to him. She focused more on the tone than the words, her fingers combing gently through his silky locks and her nails scratching lightly at his scalp. He practically purred in his strange sleep.

_He loves you._

_**And I love him.**_


End file.
